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- PDB-3ezh: Crystal Structure of the E. coli Histidine Kinase NarX Sensor Dom... -

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Basic information

Entry
Database: PDB / ID: 3ezh
TitleCrystal Structure of the E. coli Histidine Kinase NarX Sensor Domain in Complex with Nitrate
ComponentsNitrate/nitrite sensor protein narX
KeywordsTRANSFERASE / histidine kinase / sensor domain / sensor protein / four-helix bundle / nitrate sensor / selenomethionyl MAD / signal transduction / Cell inner membrane / Cell membrane / Kinase / Membrane / Nitrate assimilation / Phosphoprotein / Transmembrane / Two-component regulatory system
Function / homology
Function and homology information


cellular response to nitrate / cellular response to nitrite / histidine kinase / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / nitrate assimilation / outer membrane-bounded periplasmic space / DNA damage response / signal transduction / protein homodimerization activity ...cellular response to nitrate / cellular response to nitrite / histidine kinase / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / nitrate assimilation / outer membrane-bounded periplasmic space / DNA damage response / signal transduction / protein homodimerization activity / ATP binding / plasma membrane
Similarity search - Function
Histidine kinase NarX, sensor domain / Signal transduction histidine kinase, nitrate/nitrite-sensing / NarX-like, N-terminal domain superfamily / NarX-like, N-terminal / Type IV pili methyl-accepting chemotaxis transducer N-term / Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain / Histidine kinase / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. ...Histidine kinase NarX, sensor domain / Signal transduction histidine kinase, nitrate/nitrite-sensing / NarX-like, N-terminal domain superfamily / NarX-like, N-terminal / Type IV pili methyl-accepting chemotaxis transducer N-term / Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain / Histidine kinase / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / Histidine kinase domain / Histidine kinase domain profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
NITRATE ION / Nitrate/nitrite sensor protein NarX
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsCheung, J. / Hendrickson, W.A.
CitationJournal: Structure / Year: 2009
Title: Structural Analysis of Ligand Stimulation of the Histidine Kinase NarX.
Authors: Cheung, J. / Hendrickson, W.A.
History
DepositionOct 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jun 30, 2021Group: Data collection / Database references / Derived calculations
Category: diffrn_detector / struct_conn ...diffrn_detector / struct_conn / struct_ref_seq_dif / struct_site
Item: _diffrn_detector.detector / _struct_conn.pdbx_leaving_atom_flag ..._diffrn_detector.detector / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrate/nitrite sensor protein narX
B: Nitrate/nitrite sensor protein narX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3623
Polymers28,3002
Non-polymers621
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-4 kcal/mol
Surface area11290 Å2
MethodPISA
2
A: Nitrate/nitrite sensor protein narX
hetero molecules

A: Nitrate/nitrite sensor protein narX
hetero molecules

B: Nitrate/nitrite sensor protein narX

B: Nitrate/nitrite sensor protein narX


Theoretical massNumber of molelcules
Total (without water)56,7256
Polymers56,6014
Non-polymers1242
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
crystal symmetry operation4_455y-1/2,-x+1/2,z+1/41
crystal symmetry operation6_455x-1/2,-y+1/2,-z+1/41
Buried area6160 Å2
ΔGint-29 kcal/mol
Surface area20760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.760, 55.760, 155.257
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Nitrate/nitrite sensor protein narX


Mass: 14150.234 Da / Num. of mol.: 2 / Fragment: UNP residues 38-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Strain: K-12 / Gene: b1222, JW1213, narR, narX / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AFA2, histidine kinase
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5
Details: ammonium phosphate, pH 8.5, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9673, 0.9786, 0.9794, 0.9904
DetectorDetector: CCD / Date: Sep 22, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.96731
20.97861
30.97941
40.99041
ReflectionAv σ(I) over netI: 8.2 / Number: 128343 / Rmerge(I) obs: 0.078 / Χ2: 0.99 / D res high: 2 Å / D res low: 25 Å / Num. obs: 30963 / % possible obs: 99.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
4.32598.310.0551.886
3.424.399.110.0711.78
2.993.4298.310.0621.282
2.712.9998.910.0820.88
2.522.7199.310.1050.615
2.372.5299.310.1370.465
2.252.3799.410.1640.387
2.152.2599.510.2110.324
2.072.1599.410.2750.258
22.0799.610.3910.242
ReflectionResolution: 1.7→25 Å / Num. obs: 27197 / % possible obs: 98.4 % / Rmerge(I) obs: 0.046 / Χ2: 1.024 / Net I/σ(I): 20.1
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.760.2526480.87699
1.76-1.830.18826771.00599
1.83-1.910.14327081.05799.2
1.91-2.020.09926671.06699.1
2.02-2.140.07227261.05599.3
2.14-2.310.05726941.04599
2.31-2.540.04827261.03998.9
2.54-2.910.03927391.0398.6
2.91-3.660.03827521.02697.6
3.66-250.04228601.03494.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
DMphasing
CNS1.1refinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.7→24.94 Å / Rfactor Rfree error: 0.007 / FOM work R set: 0.818 / Data cutoff high absF: 1720149.375 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1355 5 %RANDOM
Rwork0.217 ---
obs-27155 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.202 Å2 / ksol: 0.298 e/Å3
Displacement parametersBiso mean: 32.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.23 Å20 Å20 Å2
2--5.23 Å20 Å2
3----10.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.7→24.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1819 0 4 255 2078
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_improper_angle_d1.23
X-RAY DIFFRACTIONc_mcbond_it2.521.5
X-RAY DIFFRACTIONc_mcangle_it3.222
X-RAY DIFFRACTIONc_scbond_it4.782
X-RAY DIFFRACTIONc_scangle_it6.72.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.343 202 4.8 %
Rwork0.27 3966 -
all-4168 -
obs--91.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramno3_xplor_top.txt
X-RAY DIFFRACTION3no3_xplor_par.txtwater.top

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